print STDERR "\$hystackPatt[$j] = $haystackPatt[$j]\n"; print STDERR "\$rxHaystack[$j] = $rxHaystack[$j]\n"; print STDERR "BEFORE: \$text_seqs[$i] = $text_seqs[$i]\n"; $text_seqs[$i] =~ s{$rxHaystack[$j]}{$1}gmx; print STDERR "AFTER: \$text_seqs[$i] = $text_seqs[$i]\n";